6U65 | pdb_00006u65

Mcl-1 bound to compound 19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.222 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6U65

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery and Characterization of 2,5-Substituted Benzoic Acid Dual Inhibitors of the Anti-apoptotic Mcl-1 and Bfl-1 Proteins.

Kump, K.J.Miao, L.Mady, A.S.A.Ansari, N.H.Shrestha, U.K.Yang, Y.Pal, M.Liao, C.Perdih, A.Abulwerdi, F.A.Chinnaswamy, K.Meagher, J.L.Carlson, J.M.Khanna, M.Stuckey, J.A.Nikolovska-Coleska, Z.

(2020) J Med Chem 63: 2489-2510

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01442
  • Primary Citation Related Structures: 
    6U63, 6U64, 6U65, 6U67, 6U6F

  • PubMed Abstract: 

    Anti-apoptotic Bcl-2 family proteins are overexpressed in a wide spectrum of cancers and have become well validated therapeutic targets. Cancer cells display survival dependence on individual or subsets of anti-apoptotic proteins that could be effectively targeted by multimodal inhibitors. We designed a 2,5-substituted benzoic acid scaffold that displayed equipotent binding to Mcl-1 and Bfl-1. Structure-based design was guided by several solved cocrystal structures with Mcl-1, leading to the development of compound 24 , which binds both Mcl-1 and Bfl-1 with K i values of 100 nM and shows appreciable selectivity over Bcl-2/Bcl-xL. The selective binding profile of 24 was translated to on-target cellular activity in model lymphoma cell lines. These studies lay a foundation for developing more advanced dual Mcl-1/Bfl-1 inhibitors that have potential to provide greater single agent efficacy and broader coverage to combat resistance in several types of cancer than selective Mcl-1 inhibitors alone.


  • Organizational Affiliation
    • National Institute of Chemistry, Ljubljana 1000, Slovenia.

Macromolecule Content 

  • Total Structure Weight: 74.31 kDa 
  • Atom Count: 5,112 
  • Modeled Residue Count: 603 
  • Deposited Residue Count: 624 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1
A, B, C, D
156Homo sapiensMutation(s): 0 
Gene Names: MCL1BCL2L3
UniProt & NIH Common Fund Data Resources
Find proteins for Q07820 (Homo sapiens)
Explore Q07820 
Go to UniProtKB:  Q07820
PHAROS:  Q07820
GTEx:  ENSG00000143384 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07820
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q0A
(Subject of Investigation/LOI)

Query on Q0A



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B],
N [auth C],
S [auth D]
2-[({4-[(4-fluorophenyl)methyl]piperazin-1-yl}sulfonyl)amino]-5-[(2-phenylethyl)sulfanyl]benzoic acid
C26 H28 F N3 O4 S2
WLQPDKMUGJLFLQ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
Q [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
M [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
R [auth C],
U [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
K [auth B],
L [auth B],
O [auth C],
P [auth C],
T [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
Q0A BindingDB:  6U65 Ki: 770 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.222 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.712α = 90
b = 85.223β = 90
c = 109.753γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01-CA-217141-01

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references